An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition

Daisuke Kiga, Yasuhiro Futamura, Kensaku Sakamoto, Shigeyuki Yokoyama*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

58 Citations (Scopus)


RNAs that bind to xanthine (2,6-dioxypurine) were isolated from a population of 1012 random sequences by in vitro selection. These xanthine-binding RNAs were found to have a 10 nt consensus sequence at an internal loop in the most probable secondary structure. By trimming one of the xanthine-binding RNAs, a representative xanthine-binding RNA (designated as XBA) of 32 nt residues was prepared. The dissociation constant of this RNA for xanthine was determined to be 3.3 μM by equilibrium filtration experiments. The XBA RNA can bind to guanine as well, whereas it hardly accommodates adenine, cytosine or uracil. The K(d) values for various xanthine/guanine analogues were determined, and revealed that the N1H, N7 and O6 moieties of the ligand are involved in the binding with the XBA RNA. The ribonuclease sensitivities of some internal-loop residues changed upon the addition of xanthine, suggesting that the internal loop of the XBA RNA is involved in the ligand binding. Interestingly, the consensus sequence of the xanthine/guanine-binding RNAs is the same as a sequence in one of the internal loops of the hairpin ribozyme, except for a substitution that is neutral with respect to xanthine/guanine binding.

Original languageEnglish
Pages (from-to)1755-1760
Number of pages6
JournalNucleic acids research
Issue number7
Publication statusPublished - 1998 Apr 1
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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